diff --git a/tools/restart2data.cpp b/tools/restart2data.cpp
index fd7ae62f15..cffaa67590 100644
--- a/tools/restart2data.cpp
+++ b/tools/restart2data.cpp
@@ -13,7 +13,11 @@
// Convert a LAMMPS binary restart file into an ASCII text data file
//
-// Syntax: restart2data restart-file data-file
+// Syntax: restart2data restart-file data-file (parameter-file)
+// parameter-file is optional
+// if specified it will contain LAMMPS input script commands
+// for mass and force field info
+// only a few force field styles support this option
//
// this serial code must be compiled on a platform that can read the binary
// restart file since binary formats are not compatible across all platforms
@@ -45,6 +49,9 @@ enum{VERSION,UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
enum{MASS,SHAPE,DIPOLE};
enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER};
+static const char * const cg_type_list[] =
+ {"none", "lj9_6", "lj12_4", "lj12_6"};
+
// ---------------------------------------------------------------------
// Data class to hold problem
// ---------------------------------------------------------------------
@@ -73,9 +80,13 @@ class Data {
int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
int triclinic;
+
double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;
double special_lj[4],special_coul[4];
+ double cut_lj_global,cut_coul_global,kappa;
+ int offset_flag,mix_flag;
+
// force fields
char *pair_style,*bond_style,*angle_style,*dihedral_style,*improper_style;
@@ -91,6 +102,9 @@ class Data {
double *pair_gb_epsilon,*pair_gb_sigma;
double *pair_gb_epsa,*pair_gb_epsb,*pair_gb_epsc;
double *pair_lj_epsilon,*pair_lj_sigma;
+ double **pair_cg_epsilon,**pair_cg_sigma;
+ int **pair_cg_cmm_type, **pair_setflag;
+ double **pair_cut_coul, **pair_cut_lj;
double *pair_ljexpand_epsilon,*pair_ljexpand_sigma,*pair_ljexpand_shift;
double *pair_ljsmooth_epsilon,*pair_ljsmooth_sigma;
double *pair_morse_d0,*pair_morse_alpha,*pair_morse_r0;
@@ -116,6 +130,8 @@ class Data {
double *angle_cosine_k;
double *angle_cosine_squared_k,*angle_cosine_squared_theta0;
double *angle_harmonic_k,*angle_harmonic_theta0;
+ double *angle_cg_cmm_epsilon,*angle_cg_cmm_sigma;
+ int *angle_cg_cmm_type;
double *dihedral_charmm_k,*dihedral_charmm_weight;
int *dihedral_charmm_multiplicity,*dihedral_charmm_sign;
@@ -172,7 +188,7 @@ class Data {
Data();
void stats();
- void write(FILE *);
+ void write(FILE *fp, FILE *fp2=NULL);
void write_atom_angle(FILE *, int, int, int, int);
void write_atom_atomic(FILE *, int, int, int, int);
@@ -266,13 +282,13 @@ char *read_char(FILE *fp);
// main program
// ---------------------------------------------------------------------
-main (int argc, char **argv)
+int main (int argc, char **argv)
{
// syntax error check
- if (argc != 3) {
- printf("Syntax: restart2data restart-file data-file\n");
- exit(1);
+ if ((argc != 3) && (argc !=4)) {
+ printf("Syntax: restart2data restart-file data-file [parameter-file]\n");
+ return 1;
}
// if restart file contains '%', file = filename with % replaced by "base"
@@ -297,7 +313,7 @@ main (int argc, char **argv)
FILE *fp = fopen(file,"rb");
if (fp == NULL) {
printf("ERROR: Cannot open restart file %s\n",file);
- exit(1);
+ return 1;
}
// read beginning of restart file
@@ -324,8 +340,8 @@ main (int argc, char **argv)
sprintf(file,"%s%d%s",argv[1],iproc,ptr+1);
fp = fopen(file,"rb");
if (fp == NULL) {
- printf("ERROR: Cannot open restart file %s\n",file);
- exit(1);
+ printf("ERROR: Cannot open restart file %s\n",file);
+ return 1;
}
}
n = read_int(fp);
@@ -348,17 +364,40 @@ main (int argc, char **argv)
data.stats();
- // write out data file
+ // write out data file and no parameter file
- printf("Writing data file ...\n");
- fp = fopen(argv[2],"w");
- if (fp == NULL) {
- printf("ERROR: Cannot open data file %s\n",argv[2]);
- exit(1);
+ if (argc == 3) {
+ printf("Writing data file ...\n");
+ fp = fopen(argv[2],"w");
+ if (fp == NULL) {
+ printf("ERROR: Cannot open data file %s\n",argv[2]);
+ return 1;
+ }
+ data.write(fp);
+ fclose(fp);
+
+ // write out data file and parameter file
+
+ } else {
+ printf("Writing data file ...\n");
+ fp = fopen(argv[2],"w");
+ if (fp == NULL) {
+ printf("ERROR: Cannot open data file %s\n",argv[2]);
+ return 1;
+ }
+ printf("Writing parameter file ...\n");
+ FILE *fp2 = fopen(argv[3],"w");
+ if (fp2 == NULL) {
+ printf("ERROR: Cannot open parameter file %s\n",argv[3]);
+ return 1;
+ }
+
+ data.write(fp,fp2);
+ fclose(fp);
+ fclose(fp2);
}
-
- data.write(fp);
- fclose(fp);
+
+ return 0;
}
// ---------------------------------------------------------------------
@@ -1768,6 +1807,61 @@ void pair(FILE *fp, Data &data, char *style, int flag)
}
}
+ } else if ((strcmp(style,"cg/cmm") == 0) ||
+ (strcmp(style,"cg/cmm/coul/cut") == 0) ||
+ (strcmp(style,"cg/cmm/coul/long") == 0) ) {
+ m = 0;
+ data.cut_lj_global = read_double(fp);
+ data.cut_coul_global = read_double(fp);
+ data.kappa = read_double(fp);
+ data.offset_flag = read_int(fp);
+ data.mix_flag = read_int(fp);
+
+ if (!flag) return;
+
+ const int numtyp=data.ntypes+1;
+ data.pair_cg_cmm_type = new int*[numtyp];
+ data.pair_setflag = new int*[numtyp];
+ data.pair_cg_epsilon = new double*[numtyp];
+ data.pair_cg_sigma = new double*[numtyp];
+ data.pair_cut_lj = new double*[numtyp];
+ if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
+ (strcmp(style,"cg/cmm/coul/long") == 0) ) {
+ data.pair_cut_coul = new double*[numtyp];
+ m=1;
+ } else {
+ data.pair_cut_coul = NULL;
+ m=0;
+ }
+
+ for (i = 1; i <= data.ntypes; i++) {
+ data.pair_cg_cmm_type[i] = new int[numtyp];
+ data.pair_setflag[i] = new int[numtyp];
+ data.pair_cg_epsilon[i] = new double[numtyp];
+ data.pair_cg_sigma[i] = new double[numtyp];
+ data.pair_cut_lj[i] = new double[numtyp];
+ if ((strcmp(style,"cg/cmm/coul/cut") == 0) ||
+ (strcmp(style,"cg/cmm/coul/long") == 0) ) {
+ data.pair_cut_coul[i] = new double[numtyp];
+ }
+
+ for (j = i; j <= data.ntypes; j++) {
+ itmp = read_int(fp);
+ data.pair_setflag[i][j] = itmp;
+ if (i == j && itmp == 0) {
+ printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
+ exit(1);
+ }
+ if (itmp) {
+ data.pair_cg_cmm_type[i][j] = read_int(fp);
+ data.pair_cg_epsilon[i][j] = read_double(fp);
+ data.pair_cg_sigma[i][j] = read_double(fp);
+ data.pair_cut_lj[i][j] = read_double(fp);
+ if (m) data.pair_cut_coul[i][j] = read_double(fp);
+ }
+ }
+ }
+
} else if (strcmp(style,"hybrid") == 0) {
// for each substyle of hybrid,
@@ -1922,7 +2016,8 @@ void angle(FILE *fp, Data &data)
data.angle_cosine_k = new double[data.nangletypes+1];
fread(&data.angle_cosine_k[1],sizeof(double),data.nangletypes,fp);
- } else if (strcmp(data.angle_style,"cosine/squared") == 0) {
+ } else if ((strcmp(data.angle_style,"cosine/squared") == 0) ||
+ (strcmp(data.angle_style,"cosine/delta") == 0)) {
data.angle_cosine_squared_k = new double[data.nangletypes+1];
data.angle_cosine_squared_theta0 = new double[data.nangletypes+1];
@@ -1937,6 +2032,22 @@ void angle(FILE *fp, Data &data)
fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
+ } else if (strcmp(data.angle_style,"cg/cmm") == 0) {
+
+ data.angle_harmonic_k = new double[data.nangletypes+1];
+ data.angle_harmonic_theta0 = new double[data.nangletypes+1];
+ data.angle_cg_cmm_epsilon = new double[data.nangletypes+1];
+ data.angle_cg_cmm_sigma = new double[data.nangletypes+1];
+ double *angle_cg_cmm_rcut = new double[data.nangletypes+1];
+ data.angle_cg_cmm_type = new int[data.nangletypes+1];
+
+ fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);
+ fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);
+ fread(&data.angle_cg_cmm_epsilon[1],sizeof(double),data.nangletypes,fp);
+ fread(&data.angle_cg_cmm_sigma[1],sizeof(double),data.nangletypes,fp);
+ fread(angle_cg_cmm_rcut,sizeof(double),data.nangletypes,fp);
+ fread(&data.angle_cg_cmm_type[1],sizeof(int),data.nangletypes,fp);
+
} else if (strcmp(data.angle_style,"hybrid") == 0) {
int nstyles = read_int(fp);
@@ -2243,7 +2354,7 @@ void Data::stats()
// write the data file
// ---------------------------------------------------------------------
-void Data::write(FILE *fp)
+void Data::write(FILE *fp, FILE *fp2)
{
fprintf(fp,"LAMMPS data file from restart file: timestep = %d, procs = %d\n",
ntimestep,nprocs);
@@ -2271,9 +2382,33 @@ void Data::write(FILE *fp)
fprintf(fp,"%g %g zlo zhi\n",zlo,zhi);
if (triclinic) fprintf(fp,"%g %g %g xy xz yz\n",xy,xz,yz);
+ // write ff styles to parameter file
+
+ if (fp2) {
+ fprintf(fp2,"# LAMMPS parameter file from restart file: timestep = %d, procs = %d\n\n",
+ ntimestep,nprocs);
+ if (pair_style) fprintf(fp2,"pair_style %s\n",pair_style);
+ if (bond_style) fprintf(fp2,"bond_style %s\n",bond_style);
+ if (angle_style) fprintf(fp2,"angle_style %s\n",angle_style);
+ if (dihedral_style) fprintf(fp2,"dihedral_style %s\n",dihedral_style);
+ if (improper_style) fprintf(fp2,"improper_style %s\n",improper_style);
+ fprintf(fp2,"special_bonds %g %g %g %g %g %g\n",
+ special_lj[1],special_lj[2],special_lj[3],
+ special_lj[1],special_coul[2],special_coul[3]);
+ fprintf(fp2,"\n");
+ }
+
+ // mass to either data file or parameter file
+
if (mass) {
- fprintf(fp,"\nMasses\n\n");
- for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,mass[i]);
+ if (fp2) {
+ fprintf(fp2,"\n");
+ for (int i = 1; i <= ntypes; i++) fprintf(fp2,"mass %d %g\n",i,mass[i]);
+ fprintf(fp2,"\n");
+ } else {
+ fprintf(fp,"\nMasses\n\n");
+ for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,mass[i]);
+ }
}
if (shape) {
@@ -2286,8 +2421,10 @@ void Data::write(FILE *fp)
fprintf(fp,"\nDipoles\n\n");
for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,dipole[i]);
}
-
- if (pair_style) {
+
+ // pair coeffs to data file
+
+ if (pair_style && fp2 == NULL) {
if ((strcmp(pair_style,"none") != 0) &&
(strcmp(pair_style,"eam") != 0) &&
(strcmp(pair_style,"eam/opt") != 0) &&
@@ -2389,10 +2526,41 @@ void Data::write(FILE *fp)
for (int i = 1; i <= ntypes; i++)
fprintf(fp,"%d %g\n",i,
pair_yukawa_A[i]);
+
+ } else if ((strcmp(pair_style,"cg/cmm") == 0) ||
+ (strcmp(pair_style,"cg/cmm/coul/cut") == 0) ||
+ (strcmp(pair_style,"cg/cmm/coul/long") == 0)) {
+ printf("ERROR: Cannot write pair_style %s to data file\n",
+ pair_style);
+ exit(1);
}
}
- if (bond_style) {
+ // pair coeffs to parameter file
+ // only supported styles = cg/cmm
+
+ if (pair_style && fp2) {
+ if ((strcmp(pair_style,"cg/cmm") == 0) ||
+ (strcmp(pair_style,"cg/cmm/coul/cut") == 0) ||
+ (strcmp(pair_style,"cg/cmm/coul/long") == 0)) {
+ for (int i = 1; i <= ntypes; i++) {
+ for (int j = i; j <= ntypes; j++) {
+ fprintf(fp2,"pair_coeff %d %d %s %g %g\n",i,j,
+ cg_type_list[pair_cg_cmm_type[i][j]],
+ pair_cg_epsilon[i][j],pair_cg_sigma[i][j]);
+ }
+ }
+
+ } else {
+ printf("ERROR: Cannot write pair_style %s to parameter file\n",
+ pair_style);
+ exit(1);
+ }
+ }
+
+ // bond coeffs to data file
+
+ if (bond_style && fp2 == NULL) {
if ((strcmp(bond_style,"none") != 0) &&
(strcmp(bond_style,"hybrid") != 0))
fprintf(fp,"\nBond Coeffs\n\n");
@@ -2434,7 +2602,25 @@ void Data::write(FILE *fp)
}
}
- if (angle_style) {
+ // bond coeffs to parameter file
+ // only supported styles = harmonic
+
+ if (bond_style && fp2) {
+ if (strcmp(bond_style,"harmonic") == 0) {
+ for (int i = 1; i <= nbondtypes; i++)
+ fprintf(fp2,"bond_coeff %d %g %g\n",i,
+ bond_harmonic_k[i],bond_harmonic_r0[i]);
+
+ } else {
+ printf("ERROR: Cannot write bond_style %s to parameter file\n",
+ bond_style);
+ exit(1);
+ }
+ }
+
+ // angle coeffs to data file
+
+ if (angle_style && fp2 == NULL) {
double PI = 3.1415926; // convert back to degrees
if ((strcmp(angle_style,"none") != 0) &&
@@ -2452,13 +2638,13 @@ void Data::write(FILE *fp)
fprintf(fp,"%d %g %g %g %g\n",i,
angle_class2_theta0[i]/PI*180.0,angle_class2_k2[i],
angle_class2_k3[i],angle_class2_k4[i]);
-
+
fprintf(fp,"\nBondBond Coeffs\n\n");
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g\n",i,
angle_class2_bb_k[i],
angle_class2_bb_r1[i],angle_class2_bb_r2[i]);
-
+
fprintf(fp,"\nBondAngle Coeffs\n\n");
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,
@@ -2467,13 +2653,56 @@ void Data::write(FILE *fp)
} else if (strcmp(angle_style,"cosine") == 0) {
for (int i = 1; i <= nangletypes; i++)
- fprintf(fp,"%d %g\n",i,
- angle_cosine_k[i]);
-
- } if (strcmp(angle_style,"harmonic") == 0) {
+ fprintf(fp,"%d %g\n",i,angle_cosine_k[i]);
+
+ } else if (strcmp(angle_style,"cosine/squared") == 0) {
+ for (int i = 1; i <= nangletypes; i++)
+ fprintf(fp,"%d %g %g\n",i,
+ angle_cosine_squared_k[i],
+ angle_cosine_squared_theta0[i]/PI*180.0);
+
+ } else if (strcmp(angle_style,"harmonic") == 0) {
for (int i = 1; i <= nangletypes; i++)
fprintf(fp,"%d %g %g\n",i,
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
+
+ } else if (strcmp(angle_style,"cg/cmm") == 0) {
+ for (int i = 1; i <= nangletypes; i++)
+ fprintf(fp,"%d %g %g %s %g %g\n",i,
+ angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0,
+ cg_type_list[angle_cg_cmm_type[i]],angle_cg_cmm_epsilon[i],
+ angle_cg_cmm_sigma[i]);
+ }
+ }
+
+ // angle coeffs to parameter file
+ // only supported styles = cosine/squared, harmonic, cg/cmm
+
+ if (angle_style && fp2) {
+ double PI = 3.1415926; // convert back to degrees
+
+ if (strcmp(angle_style,"cosine/squared") == 0) {
+ for (int i = 1; i <= nangletypes; i++)
+ fprintf(fp2,"angle_coeffs %d %g %g\n",i,
+ angle_cosine_squared_k[i],
+ angle_cosine_squared_theta0[i]/PI*180.0);
+
+ } else if (strcmp(angle_style,"harmonic") == 0) {
+ for (int i = 1; i <= nangletypes; i++)
+ fprintf(fp2,"angle_coeffs %d %g %g\n",i,
+ angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
+
+ } else if (strcmp(angle_style,"cg/cmm") == 0) {
+ for (int i = 1; i <= nangletypes; i++)
+ fprintf(fp2,"angle_coeffs %d %g %g %s %g %g\n",i,
+ angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0,
+ cg_type_list[angle_cg_cmm_type[i]],angle_cg_cmm_epsilon[i],
+ angle_cg_cmm_sigma[i]);
+
+ } else {
+ printf("ERROR: Cannot write angle_style %s to parameter file\n",
+ angle_style);
+ exit(1);
}
}